Evangelion Combat Evolved
by Ghost of Meat
Summary: Story under revision, see note for details.
1. Chapter 1

**Disclaimer – don't ask, don't own Eva or Halo**

**A/N after having watch the cut scenes for Halo Wars and reading both Contact Harvest and The Cole Protocol I've discovered a lot of new into on the Halo-verse so I'm doing a chapter by chapter update to this to make it more correct. And Shinji and the other children are 25 in this fic just like last time. You have no clue how many people complained that a teen would never ware the MkV armor. I know that, that's why it's been 26 years since 2****nd**** impact. I allotted that much time for a reason. More at the bottom after this chapter.**

**Evangelion – Combat Evolved**

**Chapter 1**

Flawless Cowboy

**Earth Calendar Year 2026**

**Earth, Japan Prefecture**

**Tokyo 3**

25 year old Shinji Ikari sat in the back of one of the two Pelican drop ships on its way to the Tokyo 3.

Shinji or, SPARTAN-112 as he was otherwise known, couldn't understand for the life of him why the UNSC, United Nations Space Command, would reassign one of its best trained soldiers away from the front lines.

The UNSC had been secretly formed 22 years ago to combat what is arguable the single greatest threat to humanity after second impact…

The Covenant

A collective of alien races bent on the annihilation of mankind. Claming our existence is an insult to their gods.

But it wasn't his place to question his superiors; there must be something more to this for them to order him here. According to what Intel he had, an organization with in the UN called Nerv, had requested he be sent to them. His father, Gendo Ikari, ran Nerv so he didn't think any good could come of this. He must need him to do something. Of course the existence of the UNSC was top secret information. And the SPARTAN II program, of which he was a part, was classified to the highest levels. The Marines of the UNSC knew of the SPARTANs, but only because they usually came into contact with one of the 52 known SPARTANs. Of course there were more, but only 62 total. The remainder of the group, 3 making up Gray Team and the rest known as Black Team, was on some kind of Top Secret deep cover operation. Even he wasn't able to get any details. Shinji himself was the head of Blue Team. He had been recommended for the job by SPARTAN 117; know as John, after he had been reassigned to head Black Team.

25 of the total group were KIA, leaving 37 of the original group.

Green Team, a squad of 9, had been killed when the Covenant CCS Class Curser they had boarded self destructed. Their lives hadn't been wasted though. The AI that they had taken with them, Kritos, had transmitted the schematics for the ships weapon systems to the UNSC before it exploded. That alone had tipped the balance of the war from the human race facing inevitable defeat, to a stale mate. Though it hurt to lose some of his friends, Shinji figured they would be happy with the trade off. A lot of human lives, billions in fact, had been saved.

6 SPARTANs were MIA along with the UNSC refitted Phoenix Class Colony Ship, Spirit of Fire, which had been dispatched to retake the UNSC world of Harvest at the start of the war. The ship drove the Covenant off world and set course for the Arcadia Colony and assisted in the fighting there before pursuing the Covenant forces again. She hadn't been heard from since.

The rest had been on the UNSC stronghold of Reach when the planet was glassed by the Covenant little less than 4 years ago.

He sat back in his seat. He currently held the UNSC rank of Master Chief Petty Officer, promoted to the maximum rank allowed to SPARTANs when John took command of Black Team. Currently the rest of his team was assigned to the UNSC Halcyon Class Cruiser Pillar of Autumn which was docked at the Cairo Orbital Defense Platform. He looked at the Marines who sat in the aft hold of the Pelican, checking their gear. According to Intel they were going to touch down at the main Maglev Train station at the city edge where they would meet up with a Nerv Major named Misato Katsuragi.

He shifted a bit in his MJOLNR Mk IV Armor. He was a bit nervous about having to see his father again, though his training kept his emotions in check. He checked his BR55 Battle Rifle again, then his M6 pistol. Best to be prepared.

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Gendo slammed his fist onto his desk

"This is unacceptable"

He was in a conference with the UN Secretary General; the stern mans face on the other end of the video link showed no change to his outburst

"Like it or not, as of this moment Nerv is under the command authority of the United Nations Space Command, and its heads, Fleet Admiral Andrew Whitcomb and Fleet Admiral Sir Terrence Hood. Frankly the Security Council doesn't trust you Ikari and neither do I. As of tomorrow at 1200 hours you are no longer the commander of Nerv. And before you go running of to your precious Committee, we have already taken steps concerning them; ONI is very excited about what we learned from them. There is nothing you can do about it. Admiral Whitcomb will be arriving soon to take command"

Gendo narrowed his eyes

"And what of me, I will not allow this to pass so easily, I have allies with in Nerv"

"I have ordered your office sealed from the outside, you can't leave, and currently Sub-Commander Fuyutsuki is in command and will be communicating with the Admirals to receive orders. The Lord Hood will rarely be there as his responsibilities to the Fleet come first. A UNSC Marine detachment is on route and upon their arrival will be ordered them to place you under arrest; your charges are classified as of this time. And to insure your cooperation I have sent along one of our best soldiers, SPARTAN 112, Shinji. I believe you know him"

"You've sent the third child"

"Yes, your own son will be the arresting officer, poetic justice really. It was your negligence of him which allowed the good Doctor Halsey to…how should I say this…attain him"

Gendo heard the lock bolts on the doors to his office clamp shut.

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Shinji sat in the passenger seat of one of the Warthog transports that the Pelicans had brought. They were the personnel transport type, with the rear mounted gun removed and space made in the back to hold 6 marines each. That made two squads of 8 including himself. The other squad was headed by Sergeant A.J Johnson, a marine who Shinji had served with before back when John was still with blue team.

The two Pelicans were waiting near by; having landed in the Train terminal's parking lot. Shinji's COM crackled to life, it was Cortana, a "Smart AI" created by the UNSC who had also been sent along on the Admiral's orders. She had been designed originally for the job Black Team was currently doing, infiltration behind enemy lines. But over the past year her skills had become so indispensable that UNSC High Command didn't want to risk her.

"Chief, I've got a line on the TransComm for you, its Admiral Whitcomb"

"Tell him I'll take it in the Pelican"

"Done"

He locked his BR55 onto the magnetic lock point on the back of his armor and headed to the nearest Pelican, one piloted by a very skilled pilot call signed "Foehammer".

He climbed into the Pelicans rear compartment and headed for the Communications terminal on the far wall and keyed in.

"Sierra 112 online sir"

An image of Admiral Whitcomb appeared on the screen in front of Shinji. He had a salt and pepper moustache that drooped over his upper lip and dangled off the edge of his chin. The physique of the man resembled that of a large bear. He claimed to be descendant from Russian Cossacks, despite his accent which could be best described as Texan.

"Master Chief, when you were ordered to Tokyo 3 you were told you would receive your orders upon arrival, well here they are so listen well. You and your Marines will be escorted to Nerv HQ by Major Misato Katsuragi as you know. Once there you will arrest and detain the Nerv commander Gendo Ikari and deliver him to UNSC security forces which will arrive by that time. Under no circumstances is he to be allowed to escape and should be captured alive if possible. You will then deliver Cortana to the Nerv Central Command which as of 1200 hours tomorrow will be under the command of the UNSC, myself specifically. You will personally see to it she is transferred to their computer system to assist with their operations. You will then be under the authority of the Nerv Sub-commander Kozu Fuyutsuki who will report directly to me. The Marines who are with you will insure that the facility is secure and provide security until new personnel can be sent to reinforce and remove the current Nerv Section 2 security. After which they will remain and assure base security"

Cortana then voiced what Shinji was about to.

"Sir with all due respect, shouldn't the fight with the Covenant take priority over something like this"

"The threat Nerv was originally created to face is much more potent that the Covenant at this time. Should the situation warrant however you will be transferred back to a mainline combat unit. You will receive a full briefing by Sub-Commander Fuyutsuki once you have completed this mission. Do you understand your orders Chief?"

Shinji nodded.

"Yes sir"

"Good, now go brief your Marines, Whitcomb out"

The screen in front of Shinji blanked out, he sat back for a moment in silence until Cortana then spoke up.

"You don't like this do you"

The SPARTAN shook his head.

"No, there's more going on here than he's saying"

"Well let's just go brief the Sergeant and the Marines, we'll figure it out eventually"

"Right"

Shinji jumped out of the Pelican and walked over to the two Warthogs.

"Sergeant gather the Marines, we have orders"

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Misato sped towards the Tokyo 3 primary Maglev station.

"Damn it"

She swerved around a parked car as she sped on, this was not her day.

Originally she was just supposed to pick up the commander's son, Shinji Ikari, at the station and bring him to Nerv HQ. Now she had just been told over the phone by the Sub-Commander that she was to escort Shinji and a detachment of Marines belonging to the UNSC, which she had just learned existed, to Tokyo 3. Apparently Shinji was some kind of UN super soldier or something of that nature. Ritsuko had tried to explain but couldn't say much. And to add to all, she had just been informed that Nerv was, as of noon tomorrow, under the command of the UNSC, and that there was supposedly another threat at least equal to the coming Angels.

Not her day at all.

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As Shinji finished up his briefing one of the Marines he had stationed on a near by building radioed in.

"Sir I've got one contact, it's a Blue sports car, looks like an Alpine 380. It's in bound, requesting orders sir"

"That's our escort; get your self back down here Marine"

"Yes sir"

The Marine slung his S2AM Sniper Rifle onto his back and griped the rails on the buildings fire escape and slid to the ground followed by his spotter. The pair arrived at the group as the blue Alpine rounded the corner and skidded to a stop next to one of the Pelicans.

Shinji walked up to the car as the woman inside stepped out.

"Is that her Cortana?"

"Facial recognition matches to with in .3 percent, confirmed as Nerv Major Misato Katsuragi"

He walked up to the woman whose jaw was on the ground.

"Major Katsuragi"

Misato hadn't taken here eyes off of the big guy in sage green armor since she stopped. She gulped before she answered, was THIS Shinji?

"Yeah, that's me"

He nodded and then saluted.

"Master Chief Petty Officer, SPARTAN-112 Shinji, according to our orders, your our escort to Nerv HQ"

Misato sighed and returned the salute.

"That's right"

Shinji dropped his salute and turned to Johnson.

"Let's get going Sergeant"

Johnson, acknowledging, turned to his marines.

"Alright you heard the man, let's mount it up"

As the Marines jumped into the Warthogs Shinji turned to Misato.

"It would probably be better if you rode with us. Put a 501 tag on your vehicle and let's go"

Shinji handed the 2 inch square blue tag to the Nerv Major. A 501 tag was used by UN special use vehicles to prevent towing. She put the tag on her wind shield and hoped into the back of the warthog. One of the Marines stood and held onto the bars that made up the vehicles rear roll cage so she could sit. Across from Misato sat the armor clad Shinji.

"So what orders were you given?"

He looked up at her.

"First we are to go to Nerv HQ. Second we are to arrest and detain the facility's Commander on classified charges. Third we are to deliver him to a UNSC security team which is on route. Forth I am to deliver the Smart AI Cortana to the Nerv Main Command Center and supervise her installation onto their computer systems. The marines and I will them be providing security for the facility until reinforced by a UNSC Marine company"

Misato just blinked, she hadn't been told any of that…

Yep it was going to be one of those days.

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Gendo sat back in his chair, for over 2 hours he had tried to get his computers to work.

The Magi had locked down every form of communication in the office.

He pulled his 9mm pistol from the drawer in his desk. Like hell he would go with out a fight. Maybe he would get lucky and take the third child with him. If he couldn't have what he wanted he would do as much damage as possible.

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Fuyutsuki stood on the Bridge within Nerv HQ. The coming transfer of UNSC personnel and equipment was looming in the forefront of his mind. He knew Gendo would put up a fight, what he didn't know is what he had planed.

The UNSC had granted himself and Dr Akagi immunity from prosecution if they would give written testimony against Gendo and cooperate with the UNSC. The pair had immediately agreed

Ritsuko stood by her main assistant, Maya Ibuki. Both of whom were busy erasing the personality profiles of the three Magi computers to make room for the UNSC's Smart AI Cortana. Ritsuko fumed as she entered the final line of code erasing Casper, now only the Scientist portion of her mother's personality was left. She had made backups of the original data scans though…maybe she could…with time, just maybe.

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The two warthogs pulled to a stop inside the Nerv Cargo Tram, which then set out for the GeoFront once the doors closed. The Marines had been shown an image of the GeoFront, but were still awestruck when the saw it.

But for Shinji, it was familiar, not only had he been here once, he had seen something like it elsewhere…on Reach. He killed his external communications so only Cortana could hear him.

"Cortana does this match the cavity that was found beneath the ONI Castle Base on Reach"

After a moment she responded.

"Yes chief, minus the Forerunner ruins it does. Too bad ONI didn't get a better look at them; there may have been useful technology"

Shinji nodded.

"No point worrying, that structure was leveled when Castle Base was destroyed. Log this, and once we have more Intel contact the Admiral about this"

"Yes chief"

It had taken Cortana a while to get use to Shinji. At first she questioned John's choice for his replacement. But after 6 months together even she had to concede he had made the right choice.

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The two Warthogs finally came to a stop inside the parking structure of the main HQ complex. Everyone dismounted and fell into platoon formation. Misato stood in front, looking at the marines with the Sergeant and Shinji. Sergeant Johnson spoke after everyone had fallen into formation.

"Alright men, we have been charged with the arrest and detainment of one Bastard Asshole, Gendo Ikari. We are to hold him until a UNSC security detachment from ONI can retrieve him. We are to take the target alive and as relatively unharmed as possible. But, should he try ANYTHING funny. I want you men all over it, AM I UNDERSTOOD"

All if the Marines responded.

"SIR YES SIR"

"Uh huh, damn right I am, now fall in at the doors on the double"

Each marine ran from his place and fell into 2 columns in front of the doors, the Sergeant turned to Misato and Shinji.

"Master Chief, if you and the lady would be so kind as to lead our little slumber party on"

Misato nodded, she had already served in the Military once so she knew the drill. She would be up front with Shinji immediately behind her and the Sergeant leading the Marines.

Once they were set the group set out for Gendo's office.

On the way they passed, and frightened, quite a few Nerv personnel, including Ritsuko's assistant Maya Ibuki. Misato guessed she was out for coffee. They had probably been going nonstop since the change of command orders came down from the UN.

As the doors came into sight, Misato pulled out her phone and dialed Ritsuko's number.

"Akagi"

"Listen Ritsuko, were coming to the commanders office doors now, get ready to unlock them"

She could hear Ritsuko typing while she waited for her response.

"Maya said she saw you in the hall. Who was the walking tank I saw on the security monitors"

"It was our perspective 3rd"

"Damn, alright I'm ready, just say when"

She nodded to Shinji and Johnson.

"Their ready"

The two squads of marines fell in on either side of the door. With his MJOLNR armor having an energy shield system, Shinji would be the first in, the Marines would follow with Misato bringing up the rear. Shinji looked over at Misato who had drawn her 9mm sidearm. He then turned to the Marine behind him.

"Give me your SMG"

"Yes sir"

He handed Shinji what many Marines affectionately call the "Bullet Hose". He then turned and offered the weapon to Misato.

"You have experience with the MP5K"

She nodded.

"Yeah, I spent time in the UN Counter Terrorism unit"

"This works just the same"

He pointed out the fire select lever.

"It has two fire modes, safe and full auto. You have a full magazine, 60 rounds"

Misato holstered her pistol and accepted the weapon. She extended the weapon's collapsible stock and fell into an easy ready stance at the rear of the squad on the doors right side. Some of the Marines smirked seeing her…she had done this before.

Shinji held up his left hand where everyone could see it, using his fingers he counted down from 3. Once he did he readied his weapon and the Marine directly across from him hit the door controls. As the electronic double door slid open Shinji rushed through with his BR55 Battle Rifle at the ready..

Immediately the sound of gunfire and rounds rebounding off of his shields drew his attention to the bearded man standing behind a large desk roughly 15 meters away, in front of a large glass window.

Gendo had expected to see the 3rd child in normal UN issue battle gear, not the armored form that now drew a bead on him with its rifle. He squeezed the trigger once more, the 9mm simple reflecting off of the armored soldier's energy shields.

Seeing Gendo fully intended to use lethal force Shinji immediately raised his Battle Rifle, took aim and fired. The 9.5mm round shot strait through Gendo's shoulder, spinning him around and dropping him to the floor and causing his gun to spin away from him. The bullet also passed through the window behind him, shattering it. He moved quickly toward the desk and kicked the gun away as the Marines entered and cleared the room while two of the Marines secured Gendo's hands with Zip Cuffs.

Shinji pulled a small can with a nozzle on the tip from one of his belt pouches. He shoved it into the wound in Gendo's shoulder and injected a good amount of Bio-foam into the wound. The foam would not only stop any bleeding but also disinfect the wound as well. The SPARTANs frequently used the stuff.

Sergeant Johnson and his squad then escorted Gendo to the Nerv detention block where they would stand guard until ONI arrived to retrieve him.

Misato returned the SMG to the Marine to whom it belonged, a Private Jenkins, and then walked up to Shinji who had secured his Battle Rifle to the Magnetic lock on the back of his armor.

"Nice job"

"Thanks"

"Felt good to actually get to do that again"

She continued when Shinji didn't say anything.

"Follow me, I'll take you to the bridge and introduce you to the Sub-commander"

"I need to go to the Nerv mainframe first; I have to see to Cortana's installation"

Misato nodded.

"Yeah the central computer is on the Bridge"

Shinji nodded.

"Very well, you catch that Cortana"

"Affirmative chief, not that I haven't enjoyed the ride, but I need to stretch my legs, so to speak"

Shinji had explained Cortana to Misato on the way into Nerv. The SPARTAN followed Nerv Major to the main bridge.

**A/N Zip Cuffs are the zip tie hand cuffs used by the military these days. I'll be releasing the next chapter tomorrow or the next day, once I get the bugs out.**


	2. Chapter 2

Story Notation

Ok folks quick note here, I'm redoing this fic in the light of the release of Halo Reach. So all chapters will be withdrawn when I'm ready to post the redo's. I know this breaks my rule of not redoing a fic more than twice but what the frak. So once the redo chapters are posted you will have to go back and reread the whole story as I'm going all the way back to chapter 1 and starting there.


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